Align D-trehalose PTS system, I, HPr, and IIA components (characterized)
to candidate 200507 SO1332 phosphoenolpyruvate-protein phosphotransferase PtsP (NCBI ptt file)
Query= reanno::WCS417:GFF4500 (838 letters) >FitnessBrowser__MR1:200507 Length = 744 Score = 292 bits (748), Expect = 4e-83 Identities = 201/630 (31%), Positives = 321/630 (50%), Gaps = 28/630 (4%) Query: 211 KSLVAIMALQTVQGDTLQVSAAGEDAEAAIKALVALLAEGCGEAVVNVAEPVATQSSATL 270 K++V ++ +Q Q Q S E + A +A+ G + V++ L Sbjct: 117 KAVVGVIVVQ--QASARQFSEGEEAFLMTLAAQLAMAIRGLKQKA-----QVSSLHQQIL 169 Query: 271 LRGVCASPGSAF------GQVVQVTDPELVITEQGTGGATERAALTRGLLAANEALQVLQ 324 +G AS G A G + + P++ + E L + EA+ L Sbjct: 170 FQGTSASSGIAIAHAFVLGGEISLEQPDIRCEDI----VLESNRLVAAMGRCKEAIGALS 225 Query: 325 ---DKAAGSAQAEIFRAHQELLEDPTLLEHAHRLLGEGKSAAFAWNSATLATVTLFQGLG 381 D+ A IF A Q LL+D +L R + G A A + +L + F + Sbjct: 226 QRFDREQDEEVASIFNALQLLLDDASLGGEYAREVLLGWEAESAVSRVSLRYIQQFLAME 285 Query: 382 NALIAERAADLADVGQRVLKLILGIQDSAWDLPERAILIAEQLTPSQTASLDTRKVLGFV 441 + + ERA+D+ D+GQ+VL+ ++ + + + IL+ ++ + A +K+ G V Sbjct: 286 DPYLKERASDIRDLGQKVLRQLIEPERLELEPDKPVILVTKEADATMLAEFPRQKLAGIV 345 Query: 442 TVAGGATSHVAILARALGLPAICGVPAQVLALANGKQVLLDADKGELHLEPNLAEIEQLE 501 T GG SH AILARALG+PAI GV + A + K ++++A +G+L + P+ A + + Sbjct: 346 TELGGVNSHAAILARALGVPAITGVEQLLSADIDQKLLVVNASRGQLMVSPSPAIVSEYR 405 Query: 502 AARKHQVLRHQRDVAQASLPATTRDGHHVEVTANVASLQEVEHALTLGGEGVGLLRSEFL 561 + Q ++ + +LP+ DG + + N L V + G +G+GL R+E Sbjct: 406 SLISAQKALQRQYAQELTLPSVMLDGKRIRLYLNAGLLSGVASEIAEGADGIGLYRTEIP 465 Query: 562 YLDRNRAPSPEEQAGTYTAIARALGTERNLVVRTLDVGGDKPLAYVPMDAETNPFLGLRG 621 ++ + R PS EQ Y + A + R +V+RTLDVGGDKPL Y P+ E NPFLG RG Sbjct: 466 FMLQQRFPSESEQVKVYQQVLSA-ASGRPVVMRTLDVGGDKPLPYFPI-KEDNPFLGWRG 523 Query: 622 IRLCLERPQLLREQFRAIL-ASAGFARLHIMLPMVSLLSELHLARKILEEEALAL----- 675 IRL L+ P+L Q RA+L A A +L I+LPMVS L E+ A LE+ + L Sbjct: 524 IRLSLDHPELFLVQLRAMLQAGAEGKQLSILLPMVSNLDEIDQALAYLEQAHVELKNDVN 583 Query: 676 GLTELPKLGIMIEVPSAALMADVFAPHVDFFSIGTNDLTQYTLAMDRDHPRLANQADSFH 735 ++P++GIM+EVP+ D A VDF S+G+NDLTQY LA+DR++PR+++ DS+H Sbjct: 584 SNIKMPRIGIMLEVPAMLYQLDEVAKRVDFVSVGSNDLTQYLLAVDRNNPRVSSLFDSYH 643 Query: 736 PAVLRLIATTVKAAHAHGKWVGVCGALASEALAVPVLIGLGVDELSVSVPLIPTIKATVR 795 P +LR + H + +CG LA E + +L+ +G +LS++ + I +R Sbjct: 644 PGILRALHQARLDCEYHHLDISICGELAGEPMGAILLVAMGYHQLSMNQGSLARINYLLR 703 Query: 796 ELDLADCQIIARQVLGLEEAAEVREALRQY 825 + D + Q L L +VRE +++Y Sbjct: 704 RVSGEDLAQLLAQALSLSNGFQVRELVKEY 733 Lambda K H 0.318 0.133 0.371 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 1118 Number of extensions: 44 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 838 Length of database: 744 Length adjustment: 41 Effective length of query: 797 Effective length of database: 703 Effective search space: 560291 Effective search space used: 560291 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 55 (25.8 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory